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Fluorine in PDB 5v7y: Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu

Protein crystallography data

The structure of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu, PDB code: 5v7y was solved by N.J.Schnicker, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.40 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.238, 106.826, 81.056, 90.00, 103.65, 90.00
R / Rfree (%) 16.1 / 20.9

Other elements in 5v7y:

The structure of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu (pdb code 5v7y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu, PDB code: 5v7y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5v7y

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Fluorine binding site 1 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:32.4
occ:1.00
 F1 A:TFA303 0.0 32.4 1.0
C2 A:TFA303 1.4 25.2 1.0
F2 A:TFA303 2.2 37.9 1.0
F3 A:TFA303 2.2 26.9 1.0
C1 A:TFA303 2.4 20.4 1.0
OXT A:TFA303 2.7 16.9 1.0
O A:GLY194 3.0 14.9 1.0
C A:GLY194 3.1 22.7 1.0
CG2 A:THR159 3.4 12.2 1.0
N A:GLY195 3.4 16.7 1.0
O A:TFA303 3.5 22.0 1.0
CD2 A:HIS193 3.7 15.9 1.0
CA A:GLY195 3.8 16.1 1.0
CA A:GLY194 3.9 18.0 1.0
OG1 A:THR159 4.0 10.9 1.0
CB A:THR159 4.1 13.5 1.0
N A:GLY194 4.2 13.0 1.0
CA A:THR159 4.3 11.7 1.0
NE2 A:HIS193 4.6 14.5 1.0
CG A:HIS193 4.7 15.1 1.0
C A:HIS193 4.8 15.0 1.0
N3 A:IMD302 4.8 16.2 1.0
CE1 A:HIS127 4.8 18.0 1.0
OH A:TYR118 4.9 20.1 1.0
CB A:HIS193 5.0 11.9 1.0
C4 A:IMD302 5.0 20.0 1.0

Fluorine binding site 2 out of 9 in 5v7y

Go back to Fluorine Binding Sites List in 5v7y
Fluorine binding site 2 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:37.9
occ:1.00
 F2 A:TFA303 0.0 37.9 1.0
C2 A:TFA303 1.4 25.2 1.0
F1 A:TFA303 2.2 32.4 1.0
F3 A:TFA303 2.2 26.9 1.0
C1 A:TFA303 2.4 20.4 1.0
O A:TFA303 2.7 22.0 1.0
OH A:TYR118 3.1 20.1 1.0
N A:GLY195 3.5 16.7 1.0
OXT A:TFA303 3.5 16.9 1.0
CB A:TYR124 3.6 25.7 1.0
CD2 A:TYR124 3.6 26.2 1.0
CG A:TYR124 3.8 19.9 1.0
C4 A:IMD302 3.8 20.0 1.0
CA A:GLY195 3.8 16.1 1.0
C A:GLY194 3.9 22.7 1.0
C5 A:IMD302 4.0 18.7 1.0
CE1 A:HIS127 4.1 18.0 1.0
N3 A:IMD302 4.3 16.2 1.0
CZ A:TYR118 4.4 20.9 1.0
O A:GLY194 4.4 14.9 1.0
CA A:GLY194 4.5 18.0 1.0
CE2 A:TYR124 4.6 23.4 1.0
N1 A:IMD302 4.6 12.6 1.0
C2 A:IMD302 4.7 18.9 1.0
NE2 A:HIS127 4.7 16.1 1.0
CD1 A:ILE205 4.7 11.3 1.0
CD2 A:HIS193 4.8 15.9 1.0
CO A:CO301 4.8 15.0 1.0
CD1 A:TYR124 4.9 25.0 1.0
O A:TYR124 5.0 19.8 1.0
CA A:TYR124 5.0 23.5 1.0

Fluorine binding site 3 out of 9 in 5v7y

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Fluorine binding site 3 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:26.9
occ:1.00
 F3 A:TFA303 0.0 26.9 1.0
C2 A:TFA303 1.4 25.2 1.0
F2 A:TFA303 2.2 37.9 1.0
F1 A:TFA303 2.2 32.4 1.0
C1 A:TFA303 2.3 20.4 1.0
O A:TFA303 3.0 22.0 1.0
OXT A:TFA303 3.1 16.9 1.0
C2 A:IMD302 3.3 18.9 1.0
N1 A:IMD302 3.3 12.6 1.0
N3 A:IMD302 3.5 16.2 1.0
C5 A:IMD302 3.5 18.7 1.0
C4 A:IMD302 3.6 20.0 1.0
CG2 A:VAL147 3.7 11.8 1.0
CD1 A:ILE205 3.9 11.3 1.0
CG1 A:VAL147 4.3 8.5 1.0
OH A:TYR118 4.4 20.1 1.0
CD2 A:HIS193 4.5 15.9 1.0
CO A:CO301 4.5 15.0 1.0
CB A:VAL147 4.6 9.4 1.0
CG2 A:THR159 4.6 12.2 1.0
OG1 A:THR159 4.8 10.9 1.0
NE2 A:HIS193 4.8 14.5 1.0

Fluorine binding site 4 out of 9 in 5v7y

Go back to Fluorine Binding Sites List in 5v7y
Fluorine binding site 4 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F305

b:22.3
occ:0.69
 F1 D:TFA305 0.0 22.3 0.7
C2 D:TFA305 1.3 19.3 0.7
F2 D:TFA305 2.1 24.8 0.7
F3 D:TFA305 2.1 26.2 0.7
C1 D:TFA305 2.3 11.7 0.7
O D:TFA305 2.9 10.7 0.7
OXT D:TFA305 3.1 14.3 0.7
C5 D:IMD302 3.3 23.4 1.0
C4 D:IMD302 3.3 17.3 1.0
N1 D:IMD302 3.4 17.8 1.0
N3 D:IMD302 3.5 12.6 1.0
C2 D:IMD302 3.5 12.8 1.0
CG2 D:VAL147 3.8 11.0 1.0
CD1 D:ILE205 4.1 12.7 1.0
CG1 D:VAL147 4.4 11.7 1.0
CD2 D:HIS193 4.4 10.8 1.0
CO D:CO301 4.6 12.1 1.0
OG1 D:THR159 4.6 15.3 1.0
OH D:TYR118 4.6 17.4 1.0
CB D:VAL147 4.7 11.9 1.0
CG2 D:THR159 4.7 9.1 1.0
NE2 D:HIS193 4.9 13.6 1.0

Fluorine binding site 5 out of 9 in 5v7y

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Fluorine binding site 5 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F305

b:24.8
occ:0.69
 F2 D:TFA305 0.0 24.8 0.7
C2 D:TFA305 1.3 19.3 0.7
F3 D:TFA305 2.1 26.2 0.7
F1 D:TFA305 2.1 22.3 0.7
C1 D:TFA305 2.3 11.7 0.7
O D:TFA305 2.7 10.7 0.7
O D:GLY194 3.0 13.6 1.0
C D:GLY194 3.1 17.2 1.0
N D:GLY195 3.3 16.5 1.0
OXT D:TFA305 3.4 14.3 0.7
CA D:GLY195 3.7 17.0 1.0
CG2 D:THR159 3.8 9.1 1.0
CD2 D:HIS193 3.8 10.8 1.0
CA D:GLY194 3.8 16.6 1.0
N D:GLY194 4.2 16.1 1.0
OG1 D:THR159 4.2 15.3 1.0
CB D:THR159 4.4 14.0 1.0
CA D:THR159 4.4 13.2 1.0
C5 D:IMD302 4.5 23.4 1.0
N1 D:IMD302 4.6 17.8 1.0
CG D:HIS193 4.7 12.0 1.0
C D:HIS193 4.7 16.1 1.0
CE1 D:HIS127 4.8 13.8 1.0
NE2 D:HIS193 4.8 13.6 1.0
CB D:HIS193 4.9 12.3 1.0

Fluorine binding site 6 out of 9 in 5v7y

Go back to Fluorine Binding Sites List in 5v7y
Fluorine binding site 6 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F305

b:26.2
occ:0.69
 F3 D:TFA305 0.0 26.2 0.7
C2 D:TFA305 1.3 19.3 0.7
F2 D:TFA305 2.1 24.8 0.7
F1 D:TFA305 2.1 22.3 0.7
C1 D:TFA305 2.3 11.7 0.7
OXT D:TFA305 2.7 14.3 0.7
C5 D:IMD302 3.2 23.4 1.0
OH D:TYR118 3.3 17.4 1.0
O D:TFA305 3.5 10.7 0.7
N D:GLY195 3.6 16.5 1.0
C4 D:IMD302 3.6 17.3 1.0
CB D:TYR124 3.6 20.4 1.0
CD2 D:TYR124 3.7 25.7 1.0
CG D:TYR124 3.8 16.5 1.0
N1 D:IMD302 3.9 17.8 1.0
CA D:GLY195 4.0 17.0 1.0
C D:GLY194 4.0 17.2 1.0
CE1 D:HIS127 4.1 13.8 1.0
N3 D:IMD302 4.5 12.6 1.0
O D:GLY194 4.5 13.6 1.0
CE2 D:TYR124 4.5 24.9 1.0
CA D:GLY194 4.5 16.6 1.0
CZ D:TYR118 4.6 17.4 1.0
C2 D:IMD302 4.6 12.8 1.0
CD1 D:TYR124 4.6 16.4 1.0
CD2 D:HIS193 4.7 10.8 1.0
CO D:CO301 4.8 12.1 1.0
NE2 D:HIS127 4.8 13.3 1.0
CD1 D:ILE205 5.0 12.7 1.0

Fluorine binding site 7 out of 9 in 5v7y

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Fluorine binding site 7 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F303

b:28.6
occ:1.00
 F1 C:TFA303 0.0 28.6 1.0
C2 C:TFA303 1.4 23.9 1.0
F2 C:TFA303 2.2 32.2 1.0
F3 C:TFA303 2.2 29.4 1.0
C1 C:TFA303 2.4 23.1 1.0
OXT C:TFA303 2.8 18.8 1.0
O C:GLY194 3.1 16.2 1.0
C C:GLY194 3.2 20.3 1.0
N C:GLY195 3.5 16.6 1.0
O C:TFA303 3.5 24.3 1.0
CD2 C:HIS193 3.7 15.1 1.0
CA C:GLY195 3.8 19.8 1.0
CA C:GLY194 3.8 20.6 1.0
CG2 C:THR159 3.9 11.9 1.0
N C:GLY194 4.2 22.8 1.0
OG1 C:THR159 4.3 15.8 1.0
CB C:THR159 4.5 14.9 1.0
C5 C:IMD302 4.5 21.0 1.0
NE2 C:HIS193 4.6 19.0 1.0
CE1 C:HIS127 4.6 18.2 1.0
CG C:HIS193 4.6 20.1 1.0
CA C:THR159 4.7 12.9 1.0
N1 C:IMD302 4.7 10.7 1.0
C C:HIS193 4.7 22.4 1.0
OH C:TYR118 4.9 22.4 1.0
C4 C:IMD302 4.9 18.2 1.0
CO C:CO301 4.9 16.2 1.0
CB C:HIS193 5.0 16.0 1.0
CB C:TYR124 5.0 25.8 1.0

Fluorine binding site 8 out of 9 in 5v7y

Go back to Fluorine Binding Sites List in 5v7y
Fluorine binding site 8 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F303

b:32.2
occ:1.00
 F2 C:TFA303 0.0 32.2 1.0
C2 C:TFA303 1.4 23.9 1.0
F1 C:TFA303 2.2 28.6 1.0
F3 C:TFA303 2.2 29.4 1.0
C1 C:TFA303 2.4 23.1 1.0
O C:TFA303 2.7 24.3 1.0
C5 C:IMD302 3.2 21.0 1.0
OH C:TYR118 3.2 22.4 1.0
C4 C:IMD302 3.2 18.2 1.0
OXT C:TFA303 3.5 18.8 1.0
CD2 C:TYR124 3.6 25.6 1.0
CB C:TYR124 3.8 25.8 1.0
N1 C:IMD302 3.9 10.7 1.0
CG C:TYR124 3.9 22.8 1.0
N3 C:IMD302 4.0 14.1 1.0
CE1 C:HIS127 4.1 18.2 1.0
N C:GLY195 4.2 16.6 1.0
C2 C:IMD302 4.3 19.7 1.0
CE2 C:TYR124 4.4 30.0 1.0
CA C:GLY195 4.5 19.8 1.0
C C:GLY194 4.5 20.3 1.0
CZ C:TYR118 4.5 24.4 1.0
CD1 C:ILE205 4.5 14.2 1.0
CO C:CO301 4.6 16.2 1.0
NE2 C:HIS127 4.8 20.1 1.0
CD2 C:HIS193 4.8 15.1 1.0
O C:GLY194 4.8 16.2 1.0
CD1 C:TYR124 4.9 22.4 1.0

Fluorine binding site 9 out of 9 in 5v7y

Go back to Fluorine Binding Sites List in 5v7y
Fluorine binding site 9 out of 9 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F303

b:29.4
occ:1.00
 F3 C:TFA303 0.0 29.4 1.0
C2 C:TFA303 1.4 23.9 1.0
F1 C:TFA303 2.2 28.6 1.0
F2 C:TFA303 2.2 32.2 1.0
C1 C:TFA303 2.3 23.1 1.0
OXT C:TFA303 3.0 18.8 1.0
O C:TFA303 3.2 24.3 1.0
N3 C:IMD302 3.5 14.1 1.0
C2 C:IMD302 3.5 19.7 1.0
C4 C:IMD302 3.5 18.2 1.0
CG2 C:VAL147 3.6 14.8 1.0
C5 C:IMD302 3.6 21.0 1.0
N1 C:IMD302 3.6 10.7 1.0
CG1 C:VAL147 4.0 16.0 1.0
CD1 C:ILE205 4.2 14.2 1.0
CB C:VAL147 4.3 12.6 1.0
CD2 C:HIS193 4.4 15.1 1.0
OG1 C:THR159 4.5 15.8 1.0
CG2 C:THR159 4.5 11.9 1.0
CO C:CO301 4.6 16.2 1.0
NE2 C:HIS193 4.8 19.0 1.0
OH C:TYR118 4.9 22.4 1.0

Reference:

N.J.Schnicker, M.Razzaghi, S.Guha Thakurta, S.Chakravarthy, M.Dey. Bacillus Anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry V. 56 5771 2017.
ISSN: ISSN 1520-4995
PubMed: 28981257
DOI: 10.1021/ACS.BIOCHEM.7B00601
Page generated: Thu Aug 1 15:58:17 2024

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